SNP Calling Outputs - Githubissues

salvadorlab / mbovpan

Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.

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SNP Calling Outputs #3

Closed noahaus closed 2 years ago

noahaus commented 2 years ago

When running "snp" mode, we need some basic outputs for non-bioinformatician users.

SNP table (VCF summary)
ML phylogeny

noahaus commented 2 years ago

generated the iqtree process, but want to include snp-sites into the env file 'iqtree.yaml' - current wifi is too slow. Decided to save SNP table for after submission to save time.

noahaus commented 2 years ago

Environment variable updated and capacity to run iqtree included!